Even as BofA stock has rallied, Fannie has persistently been the doubt holding back analysts from proclaiming the worst was behind BofA. The mortgage giant has been lobbing claim after claim at BofA, looking to force it to repurchase billions of dollars in mortgages Countrywide and old-time BofA sold it during the housing bubble.

The bank has said not to worry, but investors and analysts have bandied about some numbers that screamed worry.

Now Bank of America is paying Fannie $3.6 billion for its troubles and repurchasing $6.75 billion in loans, as well as delivering another payment for foreclosure delays.

It is only the latest payment BofA has made for mortgages it or Countrywide underwrote and then sold, either to the government-sponsored enterprises or to private bond investors. Two years ago this week it reached a similar deal with Freddie Mac and it has agreed to pay $8.5 billion to private bondholders in another deal.